BHARATHIAR UNIVERSITY COIMBATORE – 641 046syllabus.b-u.ac.in/unidepts/0708/ibt0708.pdf · BHARATHIAR UNIVERSITY COIMBATORE – 641 046 M.SC., INDUSTRIAL BIOTECHNOLOGY ... food and

Anx. 42 E - M. Sc. Ind. Biotech (CBCS) 2007-08 Page 1 of 32

BHARATHIAR UNIVERSITY COIMBATORE – 641 046 M.SC., INDUSTRIAL BIOTECHNOLOGY (UNIVERSITY)

FOR THE STUDENTS ADMITTED DURING THE ACADEMIC YEAR 2007 – 2008 BATCH & ONWARDS SCHEME OF EXAMINATION

University examination

Semester/ Code No.

Paper Subject Hrs per

week Dura-tion in Hrs.

Max. Marks

Cre

dits

SEM I 07BIOAC01 Paper-I Microbial diversity 4 3 100 4

07BIOAC02 Paper - II Microbial physiology and

biochemistry 4 3 100 4

07BIOAC03 Paper - III Microbial genetics and genetic

engineering 4 3 100 4

07BIOGE12 Elective 1 Bioinstrumentation and Biostatistics 4 3 100 4 Supportive 1 2 3 50 2

07BIOACP1 Practical - I Microbial techniques and genetic

engineering 6 6 100 4

SEM II 07BIOAC04 Paper – IV Bioprocess engineering 4 3 100 4 07BIOAC05 Paper – V Food biotechnology 4 3 100 4 07BIOAC06 Paper – VI Agro industrial biotechnology 4 3 100 4 07BIOGE013

Elective 2 Immunology and immunotechnology 4 3 100 4

Supportive 2 2 3 50 2

07BIOACP2 Practical –II Bioprocess, food and agroindustrial

Biotechnology 6 6 100 4

SEM III 07BIOAC07 Paper VII Biopharmaceuticals 4 3 100 4 07BIOAC08 Paper VIII Nanobiotechnology 4 3 100 4 07BIOAC09 Paper IX Industrial pollution control 07BIOGE014

Elective 3 Biosafety, Bioethics and IPR 4 4

3 3

100 100

4 4

07BIOACP3 Supportive 3 2 3 50 2 SEM IV Project viva voce* 150 6

Practical - III Biopharmaceuticals. Immunology and

industrial pollution control 6 6 100 4

Total Marks: 1,800 / 72 credits

Annexure No. 42 E SCAA Dated 29.02.2008


The following 2 diploma courses are offered and any one of the course must be selected by the candidate.

1. PG DIPLOMA IN ADVANCED LIFE SCIENCES 2. PG DIPLOMA IN COMPUTATIONAL BIOLOGY

* The report is the bonafied work carried out by the candidate under the guidance of a

faculty authenticated and countersigned by the HOD. This project work must be presented and defended by the candidate in the department attended by all faculties and reviewed by external examiner. Candidate who has presented the work as ‘Not qualified as per CBCS’ must resubmit the project again in the ensuing academic year.

COMPULSORY DIPLOMA COURSES OFFERED: (Any one is compulsory)

1. DIPLOMA IN COMPUTATIONAL BIOLOGY (UNIVERSITY) University

examination Semester

.

Paper

Subject

Hrs per week

Dura- tion in Hrs.

Max. Mark

s

Cre

dits

SEM I 07BIODA01 Computational Molecular Biology 3 3 100 4 SEM II

07BIODA02 Genomics 3 3 100 4

SEM III

07BIODA03 Proteomics 3 3 100 4

SEM IV

Practical Insilico analysis Of Nucleic acids and Proteins

3 3 100 4

2. DIPLOMA IN ADVANCED LIFE SCIENCES (UNIVERSITY)

University examination

Sem

Paper

Subject

Hrs per week

Dura-tion in Hrs.

Max. Mark

s

Cre

dits

SEM I

07BIODB01 Basic biological sciences

3

3

100 4

SEM II

07BIODB02 Biophysics, Biochemistry

&Biostatistics

3

3

100 4

SEM III

07BIODB03 Cell and molecular biology,

Immunology & Genetic Engineering

3

3

100 4

SEM IV

07BIODB04 Ecology, Physiology & Parasitology

3

3

100 4


PAPER I 07BIOA01 MICROBIAL DIVERSITY

PREAMBLE Scope This paper deals with various types of classification of microbes. The paper also throws light on multifarious habitats of microbes. Objective To impart knowledge on classification of microbes Goal This paper enables the students to identify any microorganisms. CONTENTS UNIT I SYSTEMATICS – Classical, numerical, polyphasic and molecular (G+C analysis, DNA-DNA hybridization, 16s rRNA sequencing and construction of phylogenetic tree) taxonomy; species concept in microbiology; Nomenclature (Bergey’s manual); Phylogenetic overview of prokaryotes (Bacteria,The Archaea) and eukaryotes (protozoa, fungi, slime molds, Algae) UNIT II Archae – as earliest life forms – Halophiles, methanogens, hyperthermophilic bacteria, thermoplasma Bacteria – Classification of bacteria (Bergey’s manual); salient features of each group of bacterial group Viruses – Bacterial, plant, animal and tumor viruses; Discovery, classification and structure of viruses – DNA viruses, RNA viruses, positive strands, negative strands and double stranded; replication – lytic and lysogenic UNIT III Classification of fungi (Alexopoulose); salient features of each class – habitat, cell and thallus organization; nutrition and reproduction UNIT IV Classification of algae (Smith) salient features of each class; cell and thallus organization, pigmentation, nutrition and reproduction UNIT V MICROBIAL ECOLOGY: Soil, aquatic and aerobiology; Influence of environment on microbial physiology – chemical factors; nutrients – water, C, H, O, N, P, S, growth factors- amino acids, purines, pyrimidines, nucleosides, nucleotides, vitamins, lipids, inorganic nutrients, antimicrobial compounds, metabolic inhibitors. Physical factors – radiations, temperature, pH and pressure. Response to environment – growth and reproduction; growth inhibition and death, movement, differentiation, modification to the environment – changes in chemical composition, changes in physical properties REFERENCES


1. Bergey’s manual of systematic Bacteriology – II edition, Vol 1, Springer publications.

2. Principles of Microbiology - Ronald M. Atlas, I edition Mosby - year book. inc 3. Introductory Mycology – C.J .Alexopoulose, C.W.Mims, and M . Black well IV

edition, John wiley and sons.Inc- 1996 4. Algae _ Smith 5. Methods in microbiology – C.A. Booth, Vol IV ,Academic press -1971 6. Brock Biologgy of Microorganisms – 10th edition – by MT Madigan, JM

Martinko and Jack Parker, Pearson Education Inc., NJ 7. Microbial Biotechnology - Fundamentals of applied Microbiology by A.N. Glazer

and H. Nikaido, W.H Freeman and company

8. Principles of Fermentation Technology, P.F. Stanbury & A. Whitaker, Pergamon Press.

9. Microbial Process Development by H.W Woelle, World Scientific

10. Biotechnology: Text book of Industrial Microbiology by W.Creuger and A Creuger, II edition, Sinaur associates. Inc. Sunderland.

PAPER II 07BIOA02 MICROBIAL PHYSIOLOGY AND BIOCHEMI STRY

PREAMBLE Scope This paper provides information about all the microbial cellular functions and various metabolic pathways in microbes. Objective This paper is designed to provide knowledge on metabolic function and biochemical reaction going on inside the microbial cell Goal The students will be able to understand and predict the intermediate metabolism of any microbe used in Industrial production processes CONTENTS UNIT I MOLECULAR ARCHITECHTURE: Surface appendages – Cilia and Flagella, Capsules, Pili, Fimbriae and slime layers; Cell walls – Algae, fungi, bacteria ; Structure and organization of Membrane - Model membranes (Liposomes), Glyco conjugates and proteins in membrane systems, membranes of gram positive, gram negative bacteria and acid fast bacteria, plasma membranes, intracellular membranes; Cytoplasm – constituents (tRNA, pigments, low molecular compounds); Ribosomes, Mitochondria, photosynthetic apparatus; other inclusion bodies; Mesosomes; Protoplast and spheroplast; Endospore; Genomes in prokaryotes and eukaryotes UNIT II Principles of microbial metabolism: methods used to study, microbial metabolism – nutrient balance, metabolically blocked microbes; radiolabelled compounds; transport


through membrane – solute transport process, characteristics, effect of environment; endocytosis BIOENERGETICS : Energy yielding metabolism – energy from organic compounds – carbohydrates – aerobic (EMP, HMP, ED, TCA, ET) in prokaryotes and eukaryotes; complete oxidation. Anaerobic fermentation – alcoholic fermentation, propionic acid fermentation, formic acid fermentation. UNIT III Nitrogenous compounds – catabolism of amino acids, purines and pyrimidines, triglycerides and fatty acids; Hydrocarbons – alkanes, alkenes, acyclic aromatic hydrocarbons. Aromtic compounds – tow carbon compounds, one carbon compounds, endogenous reserve polymers. Energy from inorganic compounds - ET in chemolithotrophs, production of reducing power in chemolithotrophs; Energy from visible radiation – photosynthesis in eukaryotes, blue-green algae, bacteria UNIT IV BIOSYNTHESIS: Metabolism of one carbon compounds – Calvin cycle, acetyl coA pathway, synthesis of oligosaccharides and polysaccharides. Nitrogen assimilation, nitrogen fixation, incorporation of ammonia into organic compounds (GOGAT pathway), pathways of arginine, proline, lysine, glycine, leucine and aromatic amino acids., synthesis of fatty acids and lipids UNIT V REGULATION OF METABOLISM: Synthesis of nucleotides, DNA, RNA and protein; genetic control, regulation of enzymes action; regulation of enzyme synthesis; molecular mechanism in regulation of enzyme synthesis Physiology of cell differentiation – morphological changes in vegetative organism, yeast- mycelial dimorphism, spore formation – endospores in Bacilli, ascospores in yeasts, formation of multicellular structures REFERENCES:

1. Chemical microbiology – An introduction to microbial physiology – AH Rose, Butterworth, London

2. Microbial Physiology – S. Meenakumari 3. Brock Biology of Microorganisms – 10th edition – MT Madigan, JM Martinko &

Jack Parker, Pearson and Education Inc., New Jersey

PAPER III 07BIOACO3 MICROBIAL GENETICS AND GENETIC ENGINEERING

PREAMBLE Scope The content throws light on genomic structure of microbe and various molecular tools used for genetic manipulation


Objective This paper aims to improve the knowledge on genomic structure of microbes and applications of genetic engineering Goal The students will be able to utilize this knowledge for improving the products and production process in Industries. CONTENTS UNIT I CHROMOSOME STRUCTURE AND FUNCTION: Fine structure of gene, genetic code; Genetic rearrangement – organization of coding sequences and repetitive sequences. Genetic system of bacteria – transformation, transduction, recombination; plasmids and transposons; Genetic systems of viruses – phage I, RNA viruses and retroviruses. Genetic system of fungi – Yeast and Neurospora. Genetic system of protozoa and mycoplasma UNIT II The law of DNA constancy and C - value paradox; DNA damage, mutation – types of mutation; physical and chemical mutagenesis; molecular basis of spontaneous and induced mutations, AMES test for mutagenesis; DNA repair. Recombination – homologous recombination, Holiday junction, gene targeting, gene-disruption, FL/FRT and Cre/Lox recombination, Rec A and other recombinases. Oncogenes and tumour suppressor genes – viral and cellular oncogenes, tumour suppressor genes – structure, function and mechanism of action of pRB and p53 tumour suppressor proteins UNTI III CUTTING AND JOINING OF DNA MOLECULES : Biology of vectors – plasmids, bacteriophages, single stranded DNA vectors, cosmids, phasmids, specialized vectors Cloning strategies: cloning of genomic DNA, cDNA cloning; screening strategies; differential cloning UNIT IV INTRODUCING DNA INTO BACTERIAL CELLS : Cloning in Gram negative and Gram positive bacteria, streptomycetes and fungi including Saccharomyces cerevisiae Sequencing and mutagenesis: Basic DNA sequencing, whole genome sequencing, analyzing sequence data, changing genes; site directed mutagenesis UNIT V TECHNIQUES IN GENETIC ENGINEERING : Blotting techniques – Southern, Northern and Western blotting; transformation of E. coli, PCR; probe construction, RFLP, AFLP, RAPD, SSCP and SNP. Construction of cDNA library, molecular mapping of genome – genetic and physical maps Antisense and ribozyme technology: Molecular mechanism of anti-sense molecules, inhibition of splicing, poly adenylation and translation, disruption of RNA structure and


capping. Biochemistry of Ribozyme – Hammer head, hairpin and other ribozymes; strategies for designing ribozymes; application of ribozymes and antisense technologies. REFERENCES

1. Microbial genetics – Friedfelder 2. Principles of gene manipulation – Old and Primrose 3. Genes VII by Lewine 4. Hartl. D.L. A primer of population genetics. III edition, Sinauer associates

inc. Sunderland, 2000 5. Molecular cell Biology, Darnell, Lodish, Baltimore, Scientific American

Books, Inc., 1994. 6. Molecular and cellular Biology, Stephen L.Wolfe, Wadsworth Publishing

company, 1993

PAPER IV 07BIOAC04 BIOPROCESS ENGINEERING

PREAMBLE Scope This paper provides technical information on fermenter designing and kinetics involved in the fermentation processes. Objective This paper aims to empower the students with various designs of fermenter. The growth kinetics and process kinetics of the fermentation process enable the students to manipulate for improvement Goal The students will be able to design any fermentation production processes to improve the production on completion of the paper. CONTENTS UNIT I TYPES AND DESIGN OF BIOREACTOR : Construction material; Basic components – Agitator, aerator, valves and steam traps, seals, stirrer glands; measurement and control of parameters (on-line and off line sensors) – temperature, flow rate, pressure, pH, DO, gas analysis, control pathways, computer in controlling; Air-lift, stirred tank, tower, fluidized bed, packed bed, pulsed, photo bioreactors, CSTR, PFR UNIT II PROCESS KINETICS: Kinetics of batch, fed-batch and continuous process; solid state and submerged; aerobic and anaerobic fermentation; mixed microbial populations; immobilization of cells and co-immobilization; immobilized cell reactors; Chemical kinetics and classification of chemical reactors. transport phenomena - Mass transfer, heat transfer, oxygen transfer; transfers in immobilized cells


UNIT III PRODUCTION KINETICS : Design for single and multiple reaction - size comparisons of single reactor for single reactions, multiple reactor systems for single reaction, reactions in parallel, in series, and series-parallel reactions of first order. Heterogeneous reactions, kinetics and mechanism of heterogeneous, non catalytic, and catalytic reactions; Non ideal flow - residence time distribution studies, C,E, F and I curves; RTD in ideal reactors; Models for Non ideal flow – zero – parameter model, One parameter model and two parameter model UNIT IV BIOTECHNOLOGICAL PROCESS : Isolation of microbes from various sources, Serial dilution technique, pure culture techniques and culture preservation techniques. Microbial culture collection centres. Staining techniques – Gram, endospore, negative, flagellar and methylene blue staining. Inoculum development – Development of inocula for yeast, bacterial, mycelial and vegetative fungal processes; aseptic inoculation of the fermentor Microbial growth kinetics – Batch culture, continuous culture, Fed-batch culture. Sterilization methods: Moist heat; dry heat, flame, filter, gas (ethylene oxide), Richards’ rapid method - HTST (high temperature/short time) treatments – continuous sterilizers and pasteurizers - Sterility, asepsis, Uses of UV and non-ionizing radiation. Sterilization methods – medium sterilization, batch sterilization, contiuous sterilization, filter sterilization Microbiological media: Types of media, composition of media – carbon sources, nitrogen sources, vitamins and growth factors, mineral, inducers, precursors and inhibitors. Selection and optimization of media Strain improvement methods; Recombinant cell culture process – guidelines for choosing host, vector systems, plasmid sterility in recombinant cell culture, limits to over expression UNIT V DOWN STREAM PROCESSING: Removal of microbial cells and solid matter, foam separation, precipitation, filtration, centrifugation, cell disruptions, liquid-liquid extraction, chromatography, membrane process, drying and crystallization; Quality analysis and product formulation - Product appearance, product stabilization , shelf life analysis , usage specific formulations quality analysis and control; effluent treatment and disposal REFERENCES:

1. Instrumentation, measurement and analysis, II edition (2004), Nakra BC and Chaudhry KK, Tata McGrawHill Publishing Co. Ltd., New Delhi.

2. Fermentation Microbiology and Biotechnology (2002), Mansi El-Mansi and Charlie Bryce, Taylor and Francis Ltd., London (Replika Press Pvt. Ltd., Kundli – 131 028)

3. Manual of Industrial Microbiology and Biotechnology, III edition (1999), Arnold L. Demain and Julian Davies, ASM press, Washington DC


4. Principles of Fermentation technology, Stanbury PF and Whitaker A. Pergamon Press, Oxford

5. Biochemical Engineering,Aiba,S., Humphrey, A.E. and Millis, N.F.Univ. of Tokyo Press, Tokyo.

6. Biochemical Reactors, Atkinson,B., Pion Ltd. London. 7. Biochemical Engineering Fundamentals, Baily,J.E.and Ollis,D.F., McGraw-Hill

Book Co. New york. 8. Bioprocess Technology: Fundamentals and Applications, KTH, Stockholm. 9. Process Engineering in Biotechnology, Jackson, A.T., Prentice Hall, Engelwood

Cliffs. 10. Bioprocess Engineering: Basic Concepts, Shuler,M.L. and Kargi, F., Prentice

Hall, Engelwood Cliffs. 11. Bioreaction Engineering Principles,Neilson,J. and Villadsen,J., Plenum Press. 12. Chemical Engineering Problems in Biotechnology, Shuler, M.L.(Ed.),AICHE. 13. Biochemical Engineering, Lee, J.M., Prentice Hall Inc. 14. Biochemical Engineering –Kinetics, Mass Transport, Reactors and Gene

Expression, Vieth, W.F. , John wiley and Sons, Inc. 15. Chemical reaction enginerring . Levenspiel. O. III edition, 2003. Wiley Eastern,

New Delhi 16. Elements of chemical reaction engineering. Fogler. H.S. II edition, 1992. Prentice

Hall.

PAPER V 07BIOAC05 FOOD BIOTECHNOLOGY PREAMBLE Scope This paper adds information about the role of microorganisms in many food industries both in production and spoilage processes. Objective To encode the importance of the role of microorganisms in food industries both in beneficial and harmful ways Goal The students will be able to manipulate this knowledge in prevention of spoilage and also exploit the microbes for improved food quality. CONTENTS UNIT 1 INTRODUCTION: Components of food industry; Quality factors in food- Functional groups and properties. Diet and chronic diseases. Nutritive factors of food constituents – protein, carbohydrates, fats in nutrition, bioavailability of nutrients, stability of nutrients. Microbes as direct food (Single cell protein and Baker’s yeast); mycoprotein and yeast extract; Production of starter cultures; Genetic engineering in food industry (Chymosin, Noyamyl) UNIT II FERMENTATION PRODUCTS: Dairy products: Milk processing - Cheese - principles of cheese making. Cheddar Cheese, Swiss Cheese, Surface ripened Cheeses;


Mold ripened Cheeses. Cottage and Indian Channa cheese. General principles of manufacture of Yogurt, acidophilus milk, Kefir, Koumiss Fermented foods: Soy sauce, Miso, ,Sufu, Natto, Idli, fermented fish products, Sauer Krant, pickles, fermentation of Olives, fermented sausages; Production of distilled beverage alcohol, wine, brandy and beer. UNIT III

FOOD ADDITIVES: Production of additives - organic acid (acetic acid, lactic acid and citric acid), amino acids (glutamic acid, lysine, threonine, arginine and histidine), food flavourants and pigments, nisin and bacteriocin.

UNIT IV FOOD SPOILAGE AND PRESERVATION: Food spoilage and public health - Staphylococcal, Salmonellosis, E.coli, Botulism, aflatoxin and amine production; food spoiling enzymes; Deterioration of foods; Food preservation : Principles of food preservation – methods of preservation: Physical (irradiation, drying, heat processing, chilling and freezing, high pressure and modification of atmosphere) - Chemical (Sodium benzoate Class I & II). UNIT V FOOD PROCESS TECHNOLOGY: Packaging and canning of foods – preparation for packaging, thermal processing of foods: Microwave heating, thermal inactivation of microorganisms, thermal process, evaluations, freezing and thawing of foods. Food process operations: Evaporation - single and multi effect evaporation, dehydration, psychomatric charts, drying-tunnel, tray, spray, drum, freeze; distillation. Food processing aid through biotechnology. Food Sanitation: Good manufacturing practices – Hazard analysis, Critical control points, Personnel hygiene REFERENCES

1. Industrial Microbiology, 1983, 4th Edition, Prescott and Dunn's, Gerald Reed, AVI Publishing Company Inc. Conneticut.

2. Food Biotechnology. 1982. by Knorr, D. Marcel Dekker, New York 3. Biotechnology, 1983, VI-VIII, Rehm, H.J. and Reed,G, Verlag Chemie,

Wainheim. 4. Genetic Engineering Applications for Industry, 1981, Paul,J.K.,Noyer

Corporation, New Jersey 5. Fundamentals of Food Process Engineering, 1980, Toledo,R.T., AVI

Publishing Co., USA. 6. Food Engineering Operations, 1979, 2nd Edition, Brennan,J.G., Bulters,J.R.,

Gowelx,N.D and Lilly, A.E.V., Applied Science Publishers. 7. Food Process Engineering, 1977, 2nd Edition, Heldman, D.R., AVI Publishing

Co., USA.


PAPER VI 07BIOAC06 AGRO INDUSTRIAL BIOTECHNOLOGY

PREAMBLE Scope This imparts theoretical knowledge on tissue culture techniques and transformation techniques both in plants and animals. Objective To enable the students gain information on culturing techniques and genetic manipulation of plants and animals Goal The students will be able to plan any transformation experiments in plants and animals to get newer products and new varieties. CONTENTS

UNIT I CELL AND TISSUE CULTURE IN PLANTS : Tissue culture media (composition and preparation), Genetic methods and application of superior culture; protoplast, anther, pollen, ovary and embryo culture; organogenesis, somatic embryogenesis; hardening and green house technology; synthetic seeds, germ plasm conservation; Somoclonal variation; protoplast fusion and somatic hybridization – cybrids

UNIT II TRANSGENESIS IN PLANTS: Gene transfer in plants – Gene transfer through vectors - Biology of vectors used - Ti and Ri plasmids, binary vectors, viral vectors; cloning strategy and method of gene transfer; Vectorless gene transfer – electroporation and gene gun method

Application of transgenic plants: Herbicide resistance: phosphoinothricin, glyphosate, sufonyl urea and atrazine. Insect resistance: Bt genes, non-Bt genes like protease inhibitors, alpha amylase inhibitor. Disease resistance: chitinase, 1,3-beta glucanase, RIP, antifungal proteins, thionins, PR proteins; Virus resistance: coat protein mediated, nucleocapsid gene. Nematode resistance. Abiotic stress: Drought, cold and salt. Post-harvest losses: long shelf life of fruits and flowers, use of ACC synthase, polygalacturanase, ACC oxidase, male sterile lines, bar and barnase systems, carbohydrate composition and storage, ADP glucose pyrophosphatase, RNAi and Reverse genetics. UNIT III ANIMAL CELL CULTURE TECHNIQUES : Types of cell culture - primary and established culture; organ culture; tissue culture; three dimensional culture and tissue engineering; feeder layers; disaggregation of tissue and primary cell culture; cell separation; cell synchronization; cryopreservation. Culture media- Balanced salt solutions and simple growth medium, Physical, chemical and metabolic functions of different constituents of culture medium; Role of carbon dioxide, serum, growth factors, glutamine in cell culture; Serum and protein free defined media and their applications.


UNIT IV TRANSGENESIS IN ANIMALS: cell transformation; vectorless gene transfer – calcium mediated, electroporation, electrofusion, liposome mediated gene transfer, microinjection. Gene transfer through vectors - Adenoviruses, ALVs, Bacculoviruses, SV40 Application of transgenic animals: Animals as models for human diseases, live-stock improvement, bovine growth hormone, silk worm as bioreactors UNIT V BIOTECHNOLOGY BASED SMALL SCALE INDUSTRIES : Floriculture – orchids and Bonzai techniques; Production, formulation, packing and marketing of single cell proteins (mushrooms, spirullina and yeast); Biofertilizers, BGA, Azolla, phosphobacter and vermicompost; Biopesticide – Trichoderma viridae; Food additives – colorants, flavorants, food preservatives and fruit pulp. Bio polymers, biodegradable plastics and biosurfactants. Techniques, significance and applications of sericulture, apiculture, aquaculture (fish, prawn and pearl), poultry, diary and rabbit farming

REFERENCES 1. An introduction to genetic engineering in plants, Mantel, Mathews and Mickee,

1985. Blackwell Scientific Publishers. London. 2. In Vitro culture of higher plants by R.L.M. Pierik, 1987. Martinus Nijhoff

Publisher, Dordrecht. 3. Plant cell culture. A practical approach. Second edition. Edited by R.A. Dixon and

R.A. Gonzales.1994.Oxford University Press. Oxford. 4. Plant Molecular Biology by Donald Grierson and S.V. Convey.1984. Blackie and

Son Limited. New York 5. Plant Biotechnology by Mantell, S.H and Smith, H. 1983. Cambridge University

press, UK 6. Plants, genes and agriculture by M.J. Chrispeels and D.F. Sadava.2000.The

American Scientific Publishers, USA. 7. Practical Application of Plant Molecular Biology by R.J. Henry.1997. Chapmans

and Hall. 8. Plant Biotechnology by J.Hammond, P. Mc Garvey and V. Yusibov 2000 Springer Verlag, UK 9. Plant Biotechnology and Transgenic Plants, Edited by Kirsi-Marja Oksman-

Caldentey and Wolfgang H. Barz. 2002, Marcel Dekker, Inc. New York. 10. Plant Biotechnology (The genetic manipulation of plants) by Adrian Slater, Nigel

W. Scott and Mark R. Fowler, 2003, Oxford University press, UK. 11. Molecular Plant Biology: A practical approach (Vol. I and II), Edited by Gilmartin and Bowler, 2002, Oxford University press, UK. 12. Animal cell culture; A practical approach, 4th Edition, by Freshney. R.I. John Wiley

publication. 13. Methods in cell biology; Volume 57, Animal cell culture methods, Ed. Jennie P.

Mather, David Barnes, Academic press.


14. Mammalian cell biotechnology; A practical approach, Ed. M. Butler, Oxford university press.

15. Exploring genetic mechanism; Ed. Maxine Singer and Paul Berg. 16. Principles of genetic manipulation; Ed. Old and Primrose, 6th Edition. Blackwell

science publication. 17. Biotechnoloical innovations in Animal productivity, BIOTOL Series, Butterworth –

Heineman Ltd. Oxford, 1992 18. An introduction to embryology. WB Sounders company, Philadelphia, Balinsky.

BI, 1970

PAPER VII 07BIOAC07 BIOPHARMACEUTICALS

PREAMBLE Scope This paper encodes information on drug designing, drug discovery and drug metabolism. Objective To enable the students to know the actual path of metabolism of drugs and drug discovery. Goal The information gained will help the students to formulate novel drugs.

CONTENTS UNIT I BIOLOGICAL SYSTEMS AND MODELS : Routes of administration, adsorption enhancement / solubility factor/ bioavailability, site specific delivery; Pharmacodynamics of protein therapeutics; Inter species scaling; Chemical modification of proteins/ therapeutics; Potential pitfall in tumor targeting; Colloidal particulate carrier system; Immuno suppressor in antibody therapy; Assay systems; High throughput screening; Automation; Combinatorial Synthesis: Chemistry, Biology, and Biotechnology; Genotyping: Genetic Pre-Disposition, and Heterogeneity; Pharmaco-Genomics UNIT II DRUG METABOLISM : Oxidation, reduction, hydrolysis, conjugation. Need for developing new drugs: Procedure followed in drug design; Molecular modification of lead compounds; Prodrug and soft drugs; Physico-chemical parameters in drug design; QSAR; Active site determination of enzymes; Design of enzyme inhibitors. UNIT III PHARMACOKINETICS. DRUG DISCOVERY : Substances Derived from Bacteria, Plants, Insects, and Animals; Sources of Active Principles; Assay Systems and Models (e.g., Knock-out Mice) Protein molecular modeling by computer: Docking studies; Structure based drug designing using software (Insight II LS)


UNIT IV PHARMACEUTICAL PRODUCTS: Microbial products - Antibiotics (penicillin, streptomycin, tetracycline), vitamins, probiotics. Plant secondary metabolite control mechanism and manipulation of phenyppropanoid pathway, shikimate pathway. Tissue culture production of alkaloids, flavanoids, steroids, terpenoids; animal vaccines UNIT V PHARMACEUTICAL PRODUCTS OF DNA TECHNOLOGY –Therapeutic proteins – Insulin, human growth hormone, clotting factors, interferons, interleukins, tissue plasminogen activators, erythropoietin, DNAseI, alginate lyase, muteins; Production, advantages, limitations and applications of monoclonal antibody; Oligonucleotides and Gene therapy: ras-Antisense therapy, gene delivery system; Vector usage strategies for gene therapy; Clinical trials.

REFERENCE

1. Heinrich Klefenz, “Industrial Pharmaceutical Biotechnology”, WILEY-VCH

Publication, Germany, 2002. 2. Daan Crommelin, Robert D Sindelar, “Pharmaceutical Biotechnology”, Tailor

ande Francis Publications, New york, 2002. 3. Jay P Rho, Stan G Louie, “Hand book of Pharmaceutical Biotechnology”,

Pharmaceutical products press, New york, 2003. 4. Lachman L Lieberman, HA, Kanig, J, “Theory and practice of industrial

pharmacy”, 3rd edition, Varghese publishing & Co, New Delhi,1986. 5. Remington’s Pharamaceutial sciences, 18th edtion, Mack publishing & Co.,

Easton, PA (20th Ed, 2000).

PAPER VIII 07BIOAC08 NANOBIOTECHNOLOGY

PREAMBLE Scope This provides preliminary/basic information on nano particles and its application perspectives. Objective To impart knowledge on what are nano particles and its biological applications Goal The students will be able understand the usage of nano particles for the improvement of man kind.

CONTENTS UNIT I Nano - definition, The fundamental Science behind nanotechnology- electrons, atoms and ions, molecules, metals, biosystems. Biocompataible In organic devices- Introduction, Implant coating, stems and seeds. Possibility to exploit the structures and process of biomolecules for novel functional materials, biosensors, bioelectronics in


medical applications. Introdution about protein – based nanostructures, DNA – based Nanostructures, Nanoanalysis. UNIT II Microfluidics meets Nano Lab-on-a-chip: Devices and their potential for nanobiotechnology. Definition and History, Advantages of Microfluidic Devices, concept for Microfluidic Devices, fluid transport, Stacking and sealing. Materials of Microfluidic Components. Silicon, Glass, polymers, fluid structure, fabrication methods. Surface modifications, Spotting , Detection mechanics. UNIT III Microcontacts printing of proteins: Stratigies for printing proteins on surfaces, Contact processing with hydrogel stramps, Microcontact printing, Affinity contact printing, Microcontact printing polypeptides and proteins, Printing one type of biomolecules, substrates, resolution and contrast of patterns, Activity of printed molecules, Printing multiple types of proteins, Molds and stamps, Surface chemistry, Characterization of printed patterns. UNIT IV Defined networks of Neuronal cells in vitro, physiology of information processing within Neuronal Networks, Topographical patterning, Photolithographic patterning, Photochemical patterning, Microcontact printing. UNIT V Cell - Nano structure interactions: methods and outlook. Natural Nano scale sensors. Biosensors. Biomedical applications : drugs, drug delivery, Molecular motors. Neuro electronic interfaces, protein Engineering, Nanoluminescent Tags. REFERENCES:

1. Nanotechnology a Gentle Introduction to the Next Big idea by Mark Ratner and Daniel Ratner. Pearson Education, Inc.2005.

2. Nanobiotechnology Concepts, Application and Properties by Christef M. Niemeyer, C. A. Mirkin. Wiley – Vch Publishers.

3. Nanotechnology in Biology and Medicine: Methods, devices and applications, Tuan Vo-Dinh, ISBN no. 0849329494

PAPER IX 07BIOAC09 INDUSTRIAL POLLUTION CONTROL

PREAMBLE Scope This paper imparts information about various pollution sources and preventive measures to control pollution.


Objective To provide knowledge on the effects on pollution on living systems and the means to reduce the pollution Goal The student will be able to combat any pollution problems arising from industries.

CONTENTS

UNIT I ENVIRONMENTAL BASIC CONCEPTS: Interaction between environment and biota; Concept of habitat and ecological niches; Limiting factor; Energy flow, food chain, food web and tropic levels; Ecological pyramids and recycling, biotic community-concept, structure, dominance, fluctuation and succession; N.P.C and S cycles in nature. Population ecology. Ecosystem dynamics and management: Stability and complexity of ecosystems; Speciation and extinctions; environmental impact assessment; Principles of conservation; Conservation strategies; sustainable development. Global environmental problems: ozone depletion, UV-B green house effect and acid rain, their impact in biotechnological approaches for management. UNIT II ENVIRONMENTAL POLLUTION: Types of pollution and pollution analysis – noise, air and gaseous pollution; Noise pollution : Source, measurement, impact on ecosystem and control. Air pollution : Types, source, method of sampling, measurement, impact on ecosystem and control. Control of Noise and air pollution by Biotechnological methods. Gaseous pollutants and odours: General sources, methods of control; fundamentals of adsorption, mechanism of adsorption, equilibrium isotherms, break through curve, adsorption equipment, regeneration of adsorbent, application of adsorption for control of gaseous and odour emission UNIT III Water pollution - Impurities in water, water pollution by industrial waste, examination of water, collection of water samples, water analysis – physical, chemical and biological. Standards of water quality. Water treatment processes: Primary treatment, screening, skimming with coagulants, flocculation, filteration, aeration and disinfection Secondary treatment : Aerobic processes – activated sludge, oxidation ditches, trickling filter, towers, rotating discs, rotating drums, oxidation ponds. Anaerobic digestion, anaerobic filters, Up flow anaerobic sludge blanket reactors. Tertiary treatment: Activated carbon treatment, reverse osmosis and electro dialysis. Solid waste management: sewage sludge treatment and utilization, refuse disposal, excreta disposal in unsewered area; composting and vermiculture. Radio active product waste disposal.


UNIT IV Environmental consideration in disposal of pharmaceutical compounds: Dispensing biotechnology products; Handling, professional education; Pharmaceuticals and the Environment; Biological Containment; Physical/ chemical containment; Process-Integrated Environmental Protection; Waste/Effluent Treatment and Recycling; Microbiological aspects of pharmaceutical processing – microbial spoilage and preservation; Principles of sterilization, sterilization control and sterility testing, sterile pharmaceutical products UNIT V Microbes in mining, ore leaching, oil recovery; biodegradation of noncellulosic wastes for environmental conservation and fuel; bioconversion of cellulosic wastes into protein and fuel; biodegradation of xenobiotics; bioremediation of contaminated soils and waste lands. REFERENCES: 1. Environmental Biotechnology by Alan Scragg. Pearson Education Limited,

England. 2. Environmental biotechnology by S.N. Jogdand. Himalaya Publishing House.Bombay. 3. Wastewater Engineering – Treatment, Disposal and Reuse. Metcalf and Eddy, Inc., Tata Mc Graw Hill, NewDelhi 4. Environmental chemistry by A.K. De Wiley Eastern Ltd. NewDelhi. 5. Introduction to Biodeterioration by D. Allsopp and k.J. Seal, ELBS/Edward Arnold.

ELECTIVE 1 BIOINSTRUMENTATION AND BIOSTATISTICS PREAMBLE Scope This paper imparts technical information on Instrumentation related to Biotechnology and statistical analysis. Objective This paper aims to explain the working principles of instruments Goal This will help the students to understand the functioning of the instruments and troubles shoot any problems they come across during analysis

CONTENTS UNIT I Physical techniques in proteins, nucleic acids and polysaccharide structural analysis (UV, IR, NMR, LASER, spectroscopy, MASS spectroscopy, Fluroscence Spectroscopy), Differential Calorimetry, X-ray crystallography, Ultra centrifugation, Electron Cryomicroscopy, Scanning Tunneling microscopy, X-ray crystallography, X-ray


computed tomographs (CAT Scan), Ultrasonic imagining systems, ECG, EEG, Fibre optics, sources, detectors applications, endoscope. UNIT II Tracer and other techniques, Radioactive decay, units of radioactivity, detection – Geiger-Muller counter, Scintillation counter, Autoradiography, . Applications of radio isotopes in biological and medical sciences. UNIT III Separation techniques of biomolecules – purification and criteria of homogeneity of proteins, end group analysis, hierarchy in structure. Analytical techniques in biochemistry and biophysics for small molecules and macromolecules for quantitation. Physical and chemical methods for immobilization of small and macromolecules. UNIT IV Descriptive statistics and relationship of quantitative variables: mean median mode, skewness and kurtosis, rank correlation coefficient, concurrent deviation methods, simple regression analysis. Sampling statistics and parameters – sampling distribution, students ‘t’ methods, analysis of frequencies and variance – (2 test and association of attributes , goodness of fit, ANOVA table. UNIT V Probability: events – addition, multiplication and conditional rules, counting methods, permutation and combination. Binomial distribution, Poisson distribution, Normal distribution. Design of experiments: Completely randomized design, Latin square, factorial design, confounding. Research methodology: concept prerequisites, layout, stages, format of thesis. References:

1. Instrumental methods of chemical analysis – B.K.Sharama. 2. Biophysical chemistry – Upadhyay, updhyay and Nath 3. A Biologist’s guide to principle and techniques of practical biochemistry – Brigal

L Williams 4. Handbook of Biomedical Instrumentation – R.S. Khandpur – Tata Mc GrawHill. 5. Statistical Methods – S.P.Gupta 6. Research methodology – R.C . Kothari 7. Biostatistics – A foundation for analysis in health Science - Daniel

ELECTIVE 2 IMMUNOLOGY AND IMMUNOTECHNOLOGY

PREAMBLE Scope This paper explains about the functioning of immune system in our body and the techniques related to immunology.


Objective This paper aims to impart information on how the immune system protects the body against the foreign particle information. Also provides information on the exploitation of the immune system for drug designing Goal The students will be able to understand the protection mechanism in our body which will help them in designing new products for the betterment of human kind. CONTENTS Unit I Cells of the immune system-Macrophages,Band T lymphocytes, Dendritic cellsNatural killer and Lymphockine activated killer cells, Eosinophils, neutrophils and Mast cells. Organs of the immune system:Bone marrow, Spleen, lymph nodes, MALT. Haemopoiesis and differentiation, lymphocyte trafficking. Antigen- biology, structure and functions if different classes of Immunoglobulin. Biology of Superantigens. Unit II Antigen antibody reactions, Applications of Immunological techniques, genetic control of immune response, effector mechanisms, MHC, antigen recognition and presentation, activation of B and T lymphocytes. Unit III Humoral and cell mediated immunity. Cell mediated cyatotoxicity: Mechanism of T cell and NK Cell mediated lysis, Antibody dependent cell mediated cytotoxicity and macrophage mediated cyatotoxicity.Cytokines and their role in immune regulation, Biology of Complement system,Complement fixation test and assessment of immune complexes in tissues. Immune suppression and immune tolerance. Unit IV Hyper sensitivity reactions, Autoimmune disorders, Transplantation immunology- MLR, HLA Typing, Bone marrow transplantation, Organ transplants. Immunity to Infectious agents - Bacteria, Viruses, Malaria, Anthrax and Helminthes. Tumor immunology:Tumor antigens, immune response to tumors, cancer immunotherapy, Vaccines. AIDS and other immunodeficiencaes, Strucature of HIV, envealope glycoproteins, destruction or T cells: immunologic symptoms of AIDS, AIDS vaccine ,therapy for treatment.. Unit V Vaccine technology and recombinant vaccines, Identification of B and T epitopes for vaccine development. In situ characterization of cells from tissues , Immunoscreening of Recombinant library, Hybridoma – Monoclonal Antibody, Production and applications of MAb in diagnosis and therapy, Catalytic Antibodies. FACS.


References 1. J. Kuby, 2003, Immunology 5th edition , W.H. Freeman and Company, Newyork.. 2. C.V.Rao. 2002, An Introduction to Immunology, Narosa Publishing House,

Chennai. 3. K.M.Pavri. 1996, Challenge of AIDS, National Book Trust, India. 4. I.R.Tizard, 1995, Immunology: An Introduction , 4th edition , Saunders College

Publishers, New York. 5. I.Roitt, 1994, Essential Immunology, Blackwell Science, Singapore. 6. A. Bul and K.Abbas, 1994, Cellular and Molecular immunology, W.D. Saunders

and Co, Philadelphia

ELECTIVE 3 BIOSAFETY, BIOETHICS & IPR

PREAMBLE Scope This paper provides information on ethical issues involved in biotechnology experiments. This also addresses on Biosafety aspects in Biotechnology and intellectual property rights. Objective To enable the students to know about the legal issues affecting the biotechnology research and how to establish ownership of a novel finding Goal The students will be able to understand the legal aspects involved in the biotechnology research CONTENTS UNIT I INTRODUCTION TO ETHICS/BIOETHICS – personal ethics: profession and professionalism – Moral Reasoning – Ethical theories – Person as an experimenter – Moral leadership (integrity and ingenuinity) - framework for ethical decision making; UNIT II BIOTECHNOLOGY AND ETHICS – biotechnology in agriculture and environment: benefits and risks – benefits and risks of genetic engineering – ethical aspects of genetic testing – ethical aspects relating to use of genetic information – genetic engineering and biowarfare. UNIT III ETHICAL IMPLICATIONS OF CLONING : Reproductive cloning , therapeutic cloning ; Ethical, legal and socio-economic aspects of gene therapy, germ line, somatic, embryonic and adult stem cell research- GM crops and GMO’s – biotechnology and biopiracy – ELSI of human genome project.


UNIT IV INTRODUCTION TO BIOSAFETY – biosafety issues in biotechnology – risk assessment and risk management – safety protocols: risk groups – biosafety levels – biosafety guidelines and regulations (National and International) – operation of biosafety guidelines and regulations – types of biosafety containment UNIT V INTRODUCTION TO INTELLECTUAL PROPERTY AND INTELLECT UAL PROPERTY RIGHTS – types: patents, copy rights, trade marks, design rights, geographical indications – importance of IPR – patentable and non patentables – patenting life – legal protection of biotechnological inventions – world intellectual property rights organization (WIPO) REFERENCES:

1. Principles of cloning, Jose Cibelli, Robert P. lanza, Keith H. S . Campbell, Michael D.West, Academic Press,2002Glimpses of Biodiversity – B.Bltosetti

2. Ethics in engineering, Martin. M.W. and Schinzinger.R. III Edition, Tata McGraw-Hill, New Delhi. 2003.

3. http://books.cambridge.org/0521384737.htm 4. http://online.sfsu.edu/%7Erone/GEessays/gedanger.htm 5. http://www.actahort.org/members/showpdf?booknrarnr=447_125 6. http://www.cordis.lu/elsa/src/about.htm 7. http://www.csmt.ewu.edu/csmt/chem/jcorkill/bioch480/bioLN98.html 8. http://www.accessexcellence.org/AE/AEPC/BE02/ethics/ethintro.html

PRACTICAL I : MICROBIAL TECHNIQUES AND GENETIC ENG INEERING

1. Isolation, pure culture and maintenance of aerobic and anaerobic microbes. 2. Staining techniques including fluorescent techniques 3. Identification techniques – Morphological, Biochemical and molecular techniques 4. 16S RNA typing: Phylogenetic tree construction 5. Preservation of pure culture – Lyophilisation 6. Isolation of DNA from Bacteria 7. Isolation of plasmids 8. Restriction and ligation 9. Preparation of competent cell 10. Gene transfer in microbes – calcium mediated, electroporation, vector mediated 11. Identification of recombinants – antibiotic markers, Blue-white colony 12. PCR 13. Blotting techniques –Western


PRACTICAL II BIOPROCESS, FOOD AND AGROINDUCTRIAL BIOTECHNOLOGY

1. Growth kinetics 2. Effect of pH and temperature on growth kinetics 3. Media formulation 4. Sterilization techniques 5. Strain improvement – mutation, protoplast fusion 6. Optimization OF fermentation conditions in a fermentor - Eg.Sugar to alcohol by

Experiment and by model 7. Downstream process – purification of any one protein / enzyme from fermented

broth 8. Cell and enzyme immobilization 9. Production of Cheese 10. Bread making 11. Production of wine 12. Production of citric acid 13. Mushroom cultivation 14. Colourant production – Serratia 15. Flavorant production 16. Identification of food pathogens 17. Isolation of DNA from plant cells 19. Plant tissue culture techniques – micro propagation from various ex plants:

meristematic, nodal, stem, leaf, hairy root culture 20. Agrobacterium mediated gene transfer 21. Gene transfer by micro projectile gun 22. Animal cell culture techniques 23. Microinjection – Demo in any of the advanced laboratories 24. Biofertilizers - Production and formulation of Rhizobium culture 25. Biopesticide production and formulation of Trichoderma viride 26. Sericulture and Aquaculture – visit to concern lab and report submission

PRACTICAL III BIOPHARMACEUTICALS, IMMUNOLOGY AND INDUSTRIAL POLLUTION CONTROL

1. Screening of microbes for antibiotic production 2. MIC assay of any one antibiotic – Kirby Boyer technique 3. Extraction of antioxidant from plant material and its assay 4. Blood film preparation and identification of cells 5. Methods of injection and bleeding 6. Immunization and collection of serum 7. Radial immunodiffusion 8. Double immunodiffusion 9. Immuno electrophoresis 10. Rocket immunoelectrophoresis 11. Purification of IgG from serum


12. ELISA 13. Hemolysis 14. Hemagglutination 15. Analysis of any one industrial effluent quality 16. Adsorption kinetic studies in any one metal removal process 17. Developing a treatment process for any one industrial effluent 18. Production of methane from sewage sludge 19. Production of ethanol from cellulosic waste 20. Demonstration of any one pesticide degradation process

1. COMPULSORY DIPLOMA IN COMPUTATIONAL BIOLOGY

DIPLOMA PAPER I - 07BIOAD01 - COMPUTATIONAL MOLECUL AR BIOLOGY

Preamble: Scope: To provide molecular biologists the modern molecular databases and tools including literature, sequence, structure and expression databases. Objective: To provide information an understanding of the major computational problems in the field of molecular biology. Goal: To gain knowledge on molecular databases, comparative genomics, pattern search, classification of sequence and structure, alignment of sequences, rapid similarity searching, phylogenies, automated pattern learning, representing and searching protein structure, gene expression profiling, clustering expressed genes, discovering transcription factor binding sites, discovering common functions of co-expressed genes, metabolic pathways, signal transduction pathways. Contents: Unit – I Computational Molecular Biology: Bioinformatics - Bibliographic and Full Text Journal Access - Genome Databases - Molecular Biology Databases on the Web - DNA and protein forensics analysis - Probability and statistics - Prior probability - Linkage analysis Unit - II Pattern Matching with Consensus Sequences - Quantitative & Probabilistic Pattern Matching - Sequence Alignment - Rapid Sequence Similarity Search - Near-Optimal Sequence Alignments - Multiple Sequence Alignment. Unit III Distance Based Phylogenies - Sequence Blocks & Profiles - Protein Sequence Motifs Protein Structural Motifs.


Unit IV Clustering and Functional Analysis of Coordinately Regulated Genes - Discovering Transcriptional Regulatory Signals - Ultra conservation in the Human Genome - Pathway Bioinformatics. Unit V Intro to the GCG SeqWeb Interface - Sequence Comparision - GCG SeqWeb - BestFit and Gap - Description of Progressive Pairwise Algorithm - Phylogenetic Analysis. References:

1. Bioinformatics-A beginner’s guide by Jean – Michel Claverie and Cedric Notredame, Wiley- Dream Tech India Pvt. Ltd.

2. Developing bioinformatics computer skills by Cynthia Gibas and Per Jambeck, O’ Reilly publications.

3. Introduction to bioinformatics by T.K. Attwood and D.J. Parry –smith, Pearson Education Asia.

4. Bioinformatics by David.W.Mount, CBS publishers and distributers. 5. Instant notes in bioinformatics by D.R. Westhead, J.H.Parish and R.M.Twyman. 6. Biostatistical analysis. Zar.J.H 7. Peuzner, P.A., Computational molecular Biology, An algorithmic approach.

DIPLOMA PAPER I I - 07BIOAD02 - GENOMICS

Preamble: Scope: T o provide students a detailed through background various wet lab techniques and data generation tools related to DNA sequences. Objective: To handle the data in analyzing and interepretaion including annotation. Goal: To educate students on stand alone and online software for genetic studies. Contents: Unit I Genome structure: Genome sizes and the C-value paradox, introns and exons, microbial and organelle genomes - Centromeres and telomeres, tandem repeats- dispersed repeats (transposons), gene density, intergenic DNA. Unit II Genome physical mapping and sequencing: Fragmenting the genome, the need for markers - marker sequences (RFLPs, AFLPs, SNPs, etc) - hybridization mapping -


mapping without cloning - Basic Sanger sequencing - automated sequencing- sequencing simple genomes - Sequencing large genomes - finalizing sequences – resequencing. Unit III Genome project and bioinformatics - www databases for genomes - DNA dynamics - Recombination – Evolution - Gene diversity - Consensus and pattern recognition - Sequence diversity – Polymorphism.

Unit IV Phylogenetic Genome mapping - DNA sequence database analysis - Random-shearing GenBank - Web-based ORF finding, sequence alignment and 3-D matrix tools – Genotator - DNA modeling. Unit V Orthologues and paralogues, RNA transactions, comparative genomics of viruses, bacteria, organelles and eukaryotes, lateral gene transfer. Reference: 1.The Human Genome Project; Deciphering the blueprint of heredity ; Edited by Necia Grant Cooper; University Science books, CA, USA, 1994. 2. Bioinformatics-A beginner’s guide by Jean – Michel Claverie and Cedric Notredame, Wiley- Dream Tech India Pvt. Ltd. 3. Developing bioinformatics computer skills by Cynthia Gibas and Per Jambeck, O’ Reilly publications.

DIPLOMA PAPER III - 07BIOAD02 - PROTEOMICS Scope: T o provide students a detailed through background various wet lab techniques and data generation tools related to protein sequences. Objective: To eable students to know warious wet lab and insilico tools for handling proteomic studies. Goal: To educate students on stand alone and online software for proteomic studies. Contents: Unit I Introduction to 2D gel electrophoresis, multidimensional chromatography, mass spectrometry, and analytical protein chips. Identifying proteins in complex mixtures. Protein profiling, quantitative 2DGE, quantitative mass spectrometry, Unit II The analysis of phosphoproteins and glycoproteins. Protein interaction analysis, Y2H, mass spec complex analysis, functional protein chips, protein localization, high throughput functional annotation.


Unit III Protein domains and folds, using sequences and structures to predict gene function, high throughout structural analysis of protein, structural proteomics and what it can achieve. Unit III Phamacogenomics and new drug design. Need for developing new drugs: Procedure followed in drug design; Molecular modification of lead compounds; Prodrug and soft drugs; Physico-chemical parameters in drug design; QSAR; Active site determination of enzymes; Design of enzyme inhibitors. Unit V Significance of metabolomics, methodologies, technical problems, data handling, data Interpretation. Computational protein-protein interactions RasMol – Swiss PDB viewer References 1. Branden, C and J.Troze, 1999. Introduction to protein structure. Second edition. 2. Baxevanis, A.D and Ouellette, B.F.F (Eds), 2001. Bioinformatics: A practical guide to the analysis of genes and proteins. Wiley interscience. New York. 3. Higgins, D and Taylor, W (Eds), 2000. Bioinformatics: Sequence, structure and databnks.Oxford University Press, Oxford. 4. Misener, S and Krawetz, S.A (Eds), 2001.Bioinformatics: methods and protocols. Replica press private limited, New Delhi.

07BIOADP1 - PRACTICALS IN GENOMICS AND PROTEOMICS Preamble: Scope: To become familiar with the bioinformatic tools and resources accessible via the World Wide Web for database storage, retrieval, integration and interpretation. Objective: Bioinformatics tools will be used for aligning DNA sequences for pairwise and multiple sequence comparisons, structural and functional predictions, phylogenetic construction and polymorphic characteristics that contribute to distinct metabolic responses to pharmaceuticals Goal: To gain hands on experience on molecular databases, comparative genomics, pattern search, classification of sequence and structure, alignment of sequences, rapid similarity searching, phylogenies, automated pattern learning, representing and searching protein structure, gene expression profiling, clustering expressed genes, discovering transcription factor binding sites, discovering common functions of co-expressed genes, metabolic pathways, signal transduction pathways. Contents

1. Error! Not a valid link. 2. Molecular Modeling and drug design 3. Other data bases Small molecules, Fatty acids etc.


2. COMPULSORY DIPLOMA IN LIFE SCIENCES

Semester I Diploma Paper I - Basic Biological sciences

1. Cell Biology : Structure and function of cells and intracellular organelles (of both

prokaryotes and eukaryotes) : mechanism of cell division including (mitosis and meiosis) and cell differentiation: Cell-cell interaction; Dosage compensation and mechanism of sex determination.

2. Biochemistry: Structure of atoms, molecules and chemical bonds; Principles of

physical chemistry: Thermodynamics, Kinetics, dissociation and association constants; Nucleic acid structure, genetic code, replication, transcription and translation: Structure, function and metabolism of carbohydrates, lipids and proteins; Enzymes and coenzyme; Respiration and photosynthesis.

3. Physiology: Response to stress: Active transport across membranes; Plant and

animal hormones: Nutrition (including vitamins); Reproduction in plants, microbes and animals.

4. Genetics: Principles of Mendelian inheritance, chromosome structure and function;

Gene Structure and regulation of gene expression: Linkage and genetic mapping; Extrachromosomal inheritance (episomes, mitochondria and chloraplasts); Mutation: DNA damage and repair, chromosome aberration: Transposons; Sex-linked inheritance and genetic disorders; Somatic cell genetics; Genome organisation (in both prokaryotes and eukaryotes),

5. Evolutionary Biology: Origin of life (including aspects of prebiotic environment

and molecular evolution); Concepts of evolution; Theories of organic evolution; Mechanisms of speciation; Hardyweinberg genetic equilibrium, genetic polymorphism and selection; Origin and evolution of economically important microbes, plants and animals.

6. Environmental Biology: Concept and dynamics or ecosystem, components, food

chain and energy flow, productivity and biogeochemical cycles; Types of ecosystems, Population ecology and biological control; Community structure and organisation; Environmental pollution; Sustainable development; Economic importance of microbes, plants and animals.


Semester II Diploma Paper II - Biophysics, Biochemistry & Biostatistics 1. Principles and application of light phase contrast, fluorescence, scanning and

transmission electron microscopy, Cytophotometry and flow cytometry, fixation and staining, (36). Principles of biophysical methods used for analysis of biopolymer structure, X-ray diffraction, fluorescence, UV, ORD/CD, Visible, NMR and ESR spectroscopy; Hydrodynamic methods; Atomic absorption and plasma emission spectroscopy (39).

2. Principles and applications of gel-filtration, ion-exchange and affinity

chromatography; Thin layer and gas chromatography; High pressure liquid (HPLC) chromatography; Electrophoresis and electrofocussing; Ultracentrifugation (velocity and buoyant density) (37).

3. Principles and techniques of nucleic acid hybridization and Cot curves; Sequencing

of Proteins and nucleic acids; Southern, Northern and South-Western blotting techniques; Polymerase chain reaction; Methods for measuring nucleic acid and protein interactions (38).

4. Principles and applications of tracer techniques in biology; Radiation dosimetry;

Radioactive isotopes and half life of isotopes; Effect of radiation on biological system; Autoradiography; Cerenkov radiation; Liquid scintillation spectrometry (40).

5. Primary structure of proteins and nucleic acids; Conformation of proteins and

polypeptides (secondary, Tertiary, quaternary and domain structure); Reverse turns and Ramachandran plot; Structural polymorphism of DNA, RNA and three dimensional structure of tRNA; Structure of carbohydrates, polysaccharides, glycoproteins and peptido-glycans; Helixcoil transition; Energy terms in biopolymer conformational calculation(25).

6. Biological energy transducers, Glycolysis and TCA cycle; oxidative

phosphorylations, Glycogen breakdown and synthesis; Gluconeogenesis; Interconversion of hexoses and pentoses; Amino acid metabolism; Coordinated control of metabolism; Biosynthesis of purines and pyrimidines; Oxidation of lipids; Biosynthesis of fatty acids; Triglycerides; Phospholipids; Sterols,Group transfer and Coupled reactions (26).

7. Biochemistry and molecular biology of cancer; Oncogenes; Chemical

carcinogenesis; Genetic and metabolic disorders; Hormonal imbalances; Drug metabolism and detoxification; (31).

8. Principles and practice of statistical methods in biological research, samples and

populations; Basic statistics-average, statistics of dispersion, coefficient of


variation; Standard error; Confidence limits; Probability distributions (binomial, Poisson and normal; Tests of statistical significance; Simple correlation of regression; Analysis of variance(41).

Semester III

Diploma Paper III - Cell and Molecular Biology, Immunology & Genetic Engineering 1. Structure of pro-and eukaryotic cells; Structure and organisation of membranes;

Glycoconjugates and proteins in membrane systems; Ion transport, Na+/K+ATPase; Molecular basis of signal transduction in bacteria, plants and animals; Model membranes; Liposomes; Intracellular compartments, proteinsorting, secretory and endocytic pathways; Cytoskeleton; Nucleus; Mitochondria and chloroplasts; cell cycle; Dosage compensation and sex determination and sex-linked inheritance (17).

2. The law of DNA constancy and C-value paradox; Numerical, and structural

changes in chromosomes; Molecular basis of spontaneous and induced mutations and their role in evolution; polypoidy; Environmental mutagenesis and toxicity testing; Population genetics (16)

3. Fine structure of gene, Eukaryotic genome organisation (Structure and organisation

of chromatin, polytene and lampbrush chromosomes,mitochondria and chloroplast genome organization, coding and non-coding sequences, satellite DNA); DNA damage and repair, DNA replication, amplification and Molecular recombination (28).

4. Organization of transcriptional units; Mechanism of transcription of prokaryotes

and eukaryotes; RNA processing (capping, polyadenylation, splicing, introns and exons); Ribonucleoproteins, structure of mRNA; Genetic code and protein synthesis, Ribozyme (29).

5. Regulation of gene expression in pro and eukaryotes; Attenuation and

antitermination; Operon concept; DNA methylation; Heterochromatization; Transposition; Regulatory sequences and transacting factors; Environmental regulation of gene expression (30).

6. Antigen; Structure and functions of different clauses of immunoglobulins; Primary

and secondary immune response; Lymphocytes and accessory cells; Humoral and cell mediated immunity; MHC; Mechanism of immune response and generation of immunological diversity; Genetic control of immune response, Effector mechanisms; Applications of immunological techniques, abzyme (23).

7. DNA ligases; Topoisomerases; Gyrases; Methylases; Nucleases; Restriction

endonucleases; Plasmids and bacteriophage base vectors for cDNA and genomic libraries(32).


8. Cell and tissue culture in plants and animals; Primary culture; Cell line; Cell clones;

Callus cultures; Somaclonal variation; Micropropagation; Somatic embryogenesis; Haploidy; Protoplast fusion and somatic hybridization; Cybrides; Genetransfer methods in plants and in animals; Transgenic biology; Allopheny; Artificial seeds; Hybridoma technology, Gene targeting (34). Applications of genetic engineering in agriculture, health and industry (33).

Semester IV Diploma Paper IV - Ecology, Physiology &Parasitology 1. Interactions between environment and biota; Concept of habitat and ecological

niches; Limiting factor; Energy flow, food chain, food web and tropic levels; Ecological pyramids and recycling, biotic community-concept, structure, dominance, fluctuation and succession; (18).

2. Ecosystem dynamics and management; Stability and complexity of ecosystems;

Speciation and extinctions; environmental impact assessment; Principles of conservation; Conservation strategies; sustainable development (19).

3. Water Relation; Mineral nutrition; Photosynthesis and photorespiration; Nitrogen,

Phosphorous and Sulphur metabolism; Stomatal physiology; Source and sink relationship (6).

4. Physiology and biochemistry and seed dormancy and germination; Hormonal

regulation of growth and development; Photoregulation: Growth responses, Physiology of flowering: Senescence (7).

5. Histology of mammalian organ systems, nutrition, digestion and absorption;

Circulation (open and closed circular, lymphatic systems, blood composition and function); Muscular contraction and electric organs; Excretion and osmoregulation: Nerve conduction and neurotransmitters; major sense organs and receptors; Homeostatis (neural and hormonal); Bioluminiscence; Reproduction (11).

6. Gametogenesis in animals: Molecular events during fertilization, Cleavage patterns

and fate maps, Concepts of determination, competence and induction, totipotency and nuclear transfer experiments: Cell differentiation and differential gene activity: Morphogenetic determinants in egg cytoplasm; Role of maternal contributions in early embryonic development; Genetic regulations of early embryonic development in Drosophila; Homeotic genes(12).


7. Important human and veterinary parasites (protozoans and helminths); Life cycle and biology of Plasmodium, Trypanosoma, Ascaris, Wuchereria, Fasciola, Schistosoma and Leishmania; Molecular, cellular and physiological basis of host - parasite interactions(14).

8. Arthropods and vectors of human diseases (mosquitoes, lice, flies and ticks); Mode

of transmission of pathogens by vectors,; Chemical, biological and environmental control of anthropoid vectors; Biology and control of chief insect pests of agricultural importance; Plant host-insect interaction, insect pest management; useful insects: Silkworm(15).

Assignments 1. Principles of Taxonomy as applied to the systamics and Classification of Plant

Kingdom: Taxonomic structure; Biosystematics; Plant geography; Floristics. 2. Patterns of variation in morphology and life history in plants; Broad outlines of

classification AND evolutionary trends among algae, fungi,bryophytes and pteridophytes; Principles of palaeobotany; Economic importance of algae, fungi and lichens.

3. Comparative anatomy and developmental morphology of gymnosperms and

angiosperms; Histochemical and ultrastructural aspects of development; Differentiation and morphogenesis.

4. Androgensis and gynogenesis; Breeding system; Pollination biology; structural and functional aspects of pollen and pistil; Male sterility; Self and inter-specific incompatibility; Fertilization; Embryo and seed development.

5. Plants and civilization; Centres of origin and gene diversity; Botany, utilization,

cultivation and improvement of plants of food, drug, fibre and industrial values, Unexploited plants of potential economic value; Plants as a source of renewable energy; Genetic resources and their conservation.

6. Principles of plant breeding; Important conventional methods of breeding self and

cross-pollinated and vegetatively propagated crops; Non conventional methods; Polyploidy: Genetic variability; Plant diseases and defensive mechanisms.

7. Principles of taxonomy as applied to the systematics and classification of the animal

kingdom; Classification and interrelationship amongst the major invertebrate phyla; Minor invertebrate phyla, Functional anatomy of the nonchordates; Larval forms and their evolutionary significance.

8. Classification and comparative anatomy of protochordates and chordates; Origin,

evolution and distribution of chordates groups: Adaptive radiation.


3. Physico-chemical properties of water; Kinds of aquatic habitats (fresh water and marine); Distribution of and impact of environmental factors on the aquatic biota; Productivity, mineral cycles and biodegradation in different aquatic ecosystems; Fish and Fisheries of India with respect to the management of estuarine, coastal water systems and man-made reservoirs; Biology and ecology of reservoirs(20).

9. Feeding, learning, social and sexual behavior of animals; Parental care; Circadian

rhythms; Mimicry; Migration of fishes and birds; Sociobiology; Physiological adaptation at high altitude(13).

4. Structure, classification, genetics, reproduction and physiology of bacteria and viruses (of bacteria, plants and animals); Mycoplasma protozoa and yeast (a general accounts)(21). Lysogeny and lytic cycle in bacteriophages; Bacterial transformation; Host cell

restriction; Transduction; Complementation;

Microbial fermentation; Antibiotics, organic acids and vitamins; Microbes in

decomposition and recycling processes; Symbiotic and asymbiotic N2-fixation; Microbiology of water, air, soil and sewage: Microbes as pathological agents in plants, animals and man; General design and applications of a biofermenter, Biofertilizer(22). Energy metabolism (concept of free energy); Thermodynamic principles in biology; Energy rich bonds; Weak interactions;

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BHARATHIAR UNIVERSITY COIMBATORE – 641 046syllabus.b-u.ac.in/unidepts/0708/ibt0708.pdf · BHARATHIAR UNIVERSITY COIMBATORE – 641 046 M.SC., INDUSTRIAL BIOTECHNOLOGY ... food and